Sometimes popups will be blank when Compiz is running on linux desktops. Compiz is the special effects desktop that uses 3-D hardware to make windows that glide in and wobble, This bug is noted on the Netbeans site and there is a work-around described there, look for "setting AWT_TOOLKIT to MToolkit":
http://www.netbeans.org/issues/show_bug.cgi?id=117172
(Even though Netbeans is java software, I've observed the problem with IDL.)